[gmx-users] 1-4 Interactions

toma0052 toma0052 at umn.edu
Thu Oct 19 07:33:28 CEST 2006

     I am starting simulations on a DPPC lipid bilayer taken from Peter
Tieleman's website.  Upon trying to run the energy minimization, the
program runs, but the results does not appear correct.  During the run, I
get the warning:

Warning: 1-4 interaction between 908 and 913 at distance 1.621 which is
larger than the 1-4 table size 1.000 nm.  These are ignored for the rest of
the simulation.  This usually means your system is exploding, if not, you
should increase table-extension in your mdp file.

I have tried increasing the table-extension in my em.mdp file, but I need
to increase it to over 10nm in order for that error to go away.  Could
someone explain a little bit more on what the table-extension and 1-4
interactions are, and what could possibly be wrong with my energy
minimization.  All I have done so far is to take the dppc128.pdb file and
the example2.top topology file from Peter Tieleman's site, run editconf and
grompp with en em.mdp file similar to John Kerrigan's tutorial, followed by
mdrun.  Any help would be appreciated.

Mike Tomasini

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